AdapterRemoval. This is normal and occurs when a small number of fragments < 100bp are sequencedSTAR 2.7.0d
kallisto 0.43.1.
kallisto is able to proportionally assign multi-mapping reads across both genes and transcriptsGC content of each library showing uneven and ‘spikey’ patterns. Peaks on the RHS indicate potential incomplete rRNA removal, whilst the other peaks indicate possible excessive PCR cycles and high levels of duplicated sequences.
Estimated duplication levels within each sample. Higher than expected sequence duplication rates were observed, particularly for sequences present greater than 10,000 times. Sample 179_F and 187_F were of particular concern, however this is also suggestive of incomplete rRNA removal
STAR Alignment summary showing very low levels of unique alignments, which is again suggestive of incomplete rRNA removal. Uniquely mapping reads are within the range usually seen after summarising to genes, indicating that final gene-level counts may be a little lower than is optimal.
After assignment to transcripts, the library sizes ranged between 6,954,273 and 14,565,667 reads
PCA with colours indicating treatment group and point sizes indicating sample weights. A trend from left to right along PC1 tracked somewhat with library size, with all points along PC1 appearing in order of library size for each respective treatment group. Point sizes are proportional to sample weights.
Correlation between library size and PC1. A simple regression line is also shown for illustrative purposes
Differentially expressed (DE) genes were detected using a slight variation from the common null hypothesis. Instead of testing \(H_0: \log FC = 0\) which tests for the point value zero, the null hypothesis was defined as being within the range [\(-\tau, \tau\)], with \(\tau\) set at the default value of \(\log_2 1.2\). This additionally saves filtering any detected DE based on fold-change as is common practice in many workflows.
\[ H_0: |\log FC| \leq \tau \\ vs \\ H_A: |\log FC| > \tau \]
| ID | Name | logFC | AveExpr | t | P.Value | FDR | Location |
|---|---|---|---|---|---|---|---|
| ENSRNOG00000047551 | Pnpla2 | -7.193 | 0.1297 | -13.05 | 3.334e-06 | 0.02846 | 1:213997709-214002815:(+) |
| ENSRNOG00000050004 | LOC100909761 | 6.555 | -1.417 | 12.52 | 4.326e-06 | 0.02846 | 9:37727942-37747514:(+) |
| ENSRNOG00000032832 | Mmp10 | 3.502 | 2.164 | 8.791 | 3.768e-05 | 0.1653 | 8:5734348-5742243:(+) |
| ENSRNOG00000032626 | Mmp3 | 3.614 | 4.589 | 8.206 | 5.899e-05 | 0.1738 | 8:5676665-5698579:(+) |
| ENSRNOG00000002802 | Cxcl1 | 4.896 | 1.902 | 7.857 | 8.384e-05 | 0.1738 | 14:18743685-18745457:(-) |
| ENSRNOG00000010278 | Il6 | 4.791 | 0.1518 | 7.82 | 8.594e-05 | 0.1738 | 4:3043231-3047807:(+) |
| ENSRNOG00000060849 | Rcor2 | -5.115 | -1.303 | -7.711 | 9.531e-05 | 0.1738 | 1:222519615-222524779:(+) |
| ENSRNOG00000000239 | Ccl7 | 2.753 | 2.899 | 7.269 | 0.0001174 | 0.1738 | 10:69423086-69424979:(+) |
| ENSRNOG00000007545 | Angptl4 | 1.852 | 3.859 | 7.063 | 0.0001256 | 0.1738 | 7:18627808-18634079:(-) |
| ENSRNOG00000024705 | Rarres2 | 2.478 | 4.591 | 6.78 | 0.0001754 | 0.1738 | 4:78205812-78208767:(-) |
| ENSRNOG00000015992 | Ccl20 | 4.46 | 0.1233 | 6.935 | 0.0001788 | 0.1738 | 9:88918433-88921001:(+) |
| ENSRNOG00000048321 | Tnfsf8 | 2.08 | 2.527 | 6.608 | 0.0001953 | 0.1738 | 5:79664765-79691258:(-) |
| ENSRNOG00000020953 | Ms4a7 | 1.993 | 2.448 | 6.573 | 0.0001993 | 0.1738 | 1:227490777-227506822:(-) |
| ENSRNOG00000062228 | LOC100359515 | 4.667 | 0.8863 | 6.776 | 0.0002085 | 0.1738 | 10:64762907-64790306:(-) |
| ENSRNOG00000002792 | Cxcl2 | 7.728 | 2.716 | 6.865 | 0.0002128 | 0.1738 | 14:18731378-18733391:(-) |
| ENSRNOG00000022839 | Ifit3 | 3.29 | 6.303 | 6.642 | 0.0002153 | 0.1738 | 1:252906234-252911382:(+) |
| ENSRNOG00000028043 | Cxcl3 | 6.557 | 2.794 | 6.723 | 0.0002349 | 0.1738 | 14:18820168-18839595:(-) |
| ENSRNOG00000016812 | Adamts16 | 3.1 | 0.7835 | 6.518 | 0.0002378 | 0.1738 | 1:35067490-35198939:(+) |
Average expression against logFC. Confidently significant genes (FDR < 0.05) are indicated in red, whilst others are labelled to an FDR of 20.0%
Volcano plot with confidently significant genes shown in red. Genes to an FDR of20.0%are labelled.
Expression values for genes to an FDR of 20.0%. Genes are shown in order of significance.
Given the relatively small number of DE genes, the most suitable enrichment analysis was chosen to be GSEA as this works on a ranked list with no requirement for formal consideration of genes as differentially expressed. This approach walks through a ranked list and checks to see if genes with a given gene-set are clustered at either end of the ranked list. If no correlation between the gene-set and the experiment is evident, they should be evenly spread throughout the list. Otherwise they could reasonably be expected to show directional bias. As this is a fairly broad view analysis, gene sets were chosen as defined for human EntrezGene identifiers, then these were mapped to Ensembl rat identifiers. All gene-sets are described at the Broad Institute
Four gene sets were chosen:
| Pathway | NES | \(p\) | \(p_{adj}\) | size | sizeAtMax | DE |
|---|---|---|---|---|---|---|
| HALLMARK_INTERFERON_GAMMA_RESPONSE | 1.672 | 1.153e-06 | 5.763e-05 | 181 | 37 | Il6,Ccl7,Ifit3,Ptgs2,C1s,Isg15,Sod2,Tnfaip6 |
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION | 1.828 | 1.155e-06 | 5.777e-05 | 178 | 84 | Mmp3,Il6,Cxcl6,Tgfbi |
| HALLMARK_TNFA_SIGNALING_VIA_NFKB | 1.929 | 1.158e-06 | 5.791e-05 | 175 | 87 | Il6,Tlr2,Cxcl6,Il1b,Ptgs2,Sod2,Junb,Tnfaip6,G0s2 |
| HALLMARK_MYOGENESIS | 1.781 | 1.165e-06 | 5.824e-05 | 168 | 72 | LOC108348074,Mylpf,Myh8,Tnni2,Myoz1,Myl1,Myh1,Ckm |
| HALLMARK_COMPLEMENT | 1.697 | 1.17e-06 | 5.848e-05 | 163 | 36 | Il6,Ctsl,C1s,Ctss |
| HALLMARK_INFLAMMATORY_RESPONSE | 1.934 | 1.171e-06 | 5.854e-05 | 162 | 59 | Il6,Ccl7,Tlr2,Cxcl6,Il1b,Has2,Il1r1,Tnfaip6 |
| HALLMARK_COAGULATION | 1.777 | 1.268e-06 | 6.342e-05 | 92 | 29 | Mmp3,Ctsl,Cfi,C1s |
| HALLMARK_HEME_METABOLISM | -2.071 | 7.776e-06 | 0.0003888 | 187 | 80 | |
| HALLMARK_MYC_TARGETS_V1 | -1.799 | 7.98e-06 | 0.000399 | 193 | 45 | |
| HALLMARK_E2F_TARGETS | -2.282 | 8.261e-06 | 0.000413 | 200 | 94 | |
| HALLMARK_G2M_CHECKPOINT | -2.003 | 8.303e-06 | 0.0004152 | 201 | 70 | |
| HALLMARK_HYPOXIA | 1.56 | 6.441e-05 | 0.003221 | 184 | 57 | Il6,Angptl4,Errfi1,LOC100911515,Tgfbi |
| HALLMARK_MITOTIC_SPINDLE | -1.529 | 0.0001079 | 0.005397 | 201 | 31 | |
| HALLMARK_IL6_JAK_STAT3_SIGNALING | 1.669 | 0.0001088 | 0.005442 | 79 | 24 | Il6,Ccl7,Tlr2,Il1b,Il1r2,Il1r1,Cxcl13 |
Enrichment score for the most highly ranked hallmark geneset
As this was a larger database of gene-sets, only those with between 15 & 500 genes were tested. To obtain greater statistical precision the number of permutations was increased to \(1\times10^6\).
| Pathway | NES | \(p\) | \(p_{adj}\) | size | sizeAtMax | DE |
|---|---|---|---|---|---|---|
| REN_ALVEOLAR_RHABDOMYOSARCOMA_DN | 1.771 | 1.052e-06 | 0.003661 | 400 | 117 | S100a6,Cttn,Ptges,C1s,Tspo,Tgfbi,Rhoc |
| LIM_MAMMARY_STEM_CELL_UP | 1.577 | 1.052e-06 | 0.003662 | 398 | 130 | Il6,Rarres2,Medag,Il1b,Ptgs2,Has2,Adamts1 |
| FOSTER_TOLERANT_MACROPHAGE_DN | 1.522 | 1.055e-06 | 0.003672 | 386 | 83 | Il6,Tnfsf8,Il1b,LOC497963,Errfi1,Ptgs2,Junb,Nfkbiz |
| NABA_MATRISOME_ASSOCIATED | 1.756 | 1.057e-06 | 0.003677 | 380 | 156 | Mmp3,Il6,Ccl7,Angptl4,Tnfsf8,Adamts16,Cxcl6,S100a6,Ctsl,C1qtnf7,Il1b,Slpi,Adamts15,Masp1,Adamts1,Cxcl13,Ctss,Pcsk5,LOC100911486,Ccl3 |
| HAN_SATB1_TARGETS_DN | 1.521 | 1.058e-06 | 0.00368 | 376 | 81 | Il6,Ifit3,Il1b,Ptgs2,Slpi,Tspo,Tgfbi,Pcsk5 |
| CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN | 1.623 | 1.058e-06 | 0.003681 | 375 | 116 | Ifit3,Tlr2,Cfi,Ptgs2,Slpi,C1s,Tgfbi |
| RUTELLA_RESPONSE_TO_HGF_UP | 1.563 | 1.059e-06 | 0.003685 | 372 | 106 | Il1b,Il1r2,C1s,Sod2,Il1r1,Tnfaip6,Ccl3 |
| BOQUEST_STEM_CELL_CULTURED_VS_FRESH_UP | 1.678 | 1.059e-06 | 0.003686 | 371 | 120 | Angptl4,Cfi,LOC108348074,Prg4,Sod2,Junb,Tnfaip6,Ctss |
| DELYS_THYROID_CANCER_UP | 1.61 | 1.064e-06 | 0.003701 | 355 | 105 | Tlr2,Cttn,Slpi,Has2,Tnfaip6,Ctss,G0s2,Tspo,Ccl3 |
| LINDGREN_BLADDER_CANCER_CLUSTER_2B | 1.616 | 1.065e-06 | 0.003706 | 351 | 96 | Rarres2,LOC108348074,C1s,Nfkbiz |
| SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP | 1.737 | 1.076e-06 | 0.003744 | 318 | 117 | Mmp3,Rarres2,LOC108348074,C1s,Il1r1,Tnfaip6,Ctss,Tgfbi |
| RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN | 1.633 | 1.082e-06 | 0.003767 | 300 | 97 | S100a6,Adamts15 |
| PASINI_SUZ12_TARGETS_DN | 1.598 | 1.092e-06 | 0.0038 | 277 | 106 | S100a6,Errfi1 |
| WANG_SMARCE1_TARGETS_UP | 1.794 | 1.117e-06 | 0.003888 | 229 | 88 | Ifit3,Cfi,LOC108348074,Car4,C1s,Prg4,Il1r1,Tgfbi |
| HOSHIDA_LIVER_CANCER_SUBCLASS_S1 | 1.662 | 1.121e-06 | 0.003901 | 223 | 61 | LOC108348074,Ctss,Ccl3 |
| BOQUEST_STEM_CELL_UP | 1.677 | 1.125e-06 | 0.003914 | 217 | 85 | C1s,Tnfaip6 |
| VERHAAK_GLIOBLASTOMA_MESENCHYMAL | 1.708 | 1.126e-06 | 0.00392 | 215 | 90 | Tlr2,Il1r1,Tgfbi |
| MCLACHLAN_DENTAL_CARIES_UP | 1.676 | 1.13e-06 | 0.003933 | 210 | 72 | Il6,Cfi,Il1b,LOC108348074,Ptgs2,Slpi,Sod2,Cxcl13,Tnfaip6,Ctss,G0s2,Ccl3 |
| MARKEY_RB1_ACUTE_LOF_DN | 1.67 | 1.135e-06 | 0.00395 | 203 | 56 | Mmp3,Ccl7,Ifit3,Isg15,Sod2,Tgfbi,Pcsk5,Ccl3 |
| PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP | 1.725 | 1.149e-06 | 0.003997 | 186 | 68 | Rarres2,LOC108348074,C1s,Adamts1 |
| ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF | 1.686 | 1.151e-06 | 0.004006 | 183 | 68 | Il6,Il1b,Ptgs2,Junb,Nfkbiz |
| ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP | 1.745 | 1.155e-06 | 0.004021 | 178 | 59 | Ifit3,Tlr2,Il1b,Il1r2,Sod2,Tnfaip6,G0s2,Nfkbiz |
| BROWN_MYELOID_CELL_DEVELOPMENT_UP | 1.864 | 1.181e-06 | 0.004109 | 152 | 48 | Tlr2,S100a6,Il1b,Il1r2,Junb,Ctss,Tgfbi |
| GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_UP | 1.733 | 1.2e-06 | 0.004175 | 135 | 50 | Angptl4,Errfi1,Vwa1,LOC100911515,Nfkbiz |
| NABA_ECM_REGULATORS | 1.77 | 1.201e-06 | 0.00418 | 134 | 61 | Mmp3,Adamts16,Ctsl,Slpi,Adamts15,Masp1,Adamts1,Ctss,Pcsk5 |
| MIKKELSEN_MEF_LCP_WITH_H3K4ME3 | 1.829 | 1.232e-06 | 0.004289 | 112 | 51 | Ccl7,Masp1 |
| ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION | 1.985 | 1.235e-06 | 0.004298 | 110 | 50 | Il6,Tlr2,Cxcl6,Il1b,Il1r2,Isg15,Sod2,Junb,Nfkbiz,Ccl3 |
| HOLLERN_EMT_BREAST_TUMOR_UP | 1.803 | 1.247e-06 | 0.004339 | 103 | 39 | Medag |
| GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN | 1.86 | 1.293e-06 | 0.0045 | 80 | 42 | Il1b,Errfi1,Ptgs2,Junb,Ccl3 |
| HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN | 1.826 | 1.309e-06 | 0.004556 | 73 | 32 | Tlr2,Il1b,Il1r2,Car4,Ctss,Tgfbi |
| SANA_TNF_SIGNALING_UP | 1.874 | 1.337e-06 | 0.004653 | 63 | 22 | Mmp3,Ccl7,Tlr2,Cxcl6,C1s,Sod2 |
| LINDSTEDT_DENDRITIC_CELL_MATURATION_A | 1.888 | 1.375e-06 | 0.004786 | 51 | 25 | Il6,Tlr2,Il1b,Isg15,Sod2,Ccl3 |
| RICKMAN_HEAD_AND_NECK_CANCER_F | 1.929 | 1.394e-06 | 0.004851 | 46 | 34 | LOC100909761,Mylpf,Mybpc2,Tnni2,Myl1,Myh1,Ckm |
| THUM_SYSTOLIC_HEART_FAILURE_UP | 1.506 | 2.118e-06 | 0.007371 | 371 | 98 | Cfi,C1s,Ctss |
| ROZANOV_MMP14_TARGETS_UP | 1.617 | 2.229e-06 | 0.007756 | 234 | 79 | Tlr2,Aldh18a1,Il1r2,Errfi1,Has2,Il1r1 |
| VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP | 1.705 | 2.377e-06 | 0.008271 | 145 | 55 | Il6,Tlr2,LOC108348074,Sod2,Tnfaip6 |
| GROSS_HYPOXIA_VIA_ELK3_DN | 1.708 | 2.381e-06 | 0.008287 | 143 | 48 | Il6,Cxcl6,Errfi1,Ptgs2,Slpi,Vwa1 |
| JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP | 1.805 | 2.662e-06 | 0.009265 | 65 | 24 | Ifit3,Cxcl6,Slpi,Isg15 |
| NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP | 1.823 | 2.668e-06 | 0.009286 | 64 | 33 | S100a6,C1s,Tnfaip6 |
Enrichment score for the most highly ranked C2 geneset As this peak was relatively far from the significantly DE genes, this is not a partiularly compelling result
| Pathway | NES | \(p\) | \(p_{adj}\) | size | sizeAtMax | DE |
|---|---|---|---|---|---|---|
| GO_CELLULAR_RESPONSE_TO_CYTOKINE_STIMULUS | 1.659 | 1.041e-06 | 0.004111 | 452 | 125 | Il6,Ccl7,Ifit3,Cxcl6,Il1b,Il1r2,Arg1,LOC497963,Has2,Isg15,Il1r1,Cxcl13,Ccl3 |
| GO_CALCIUM_ION_BINDING | 1.534 | 1.046e-06 | 0.004129 | 427 | 138 | Mmp3,S100a6,Mylpf,C1s,Masp1,Myl1,LOC100911692,LOC100911486 |
| GO_INNATE_IMMUNE_RESPONSE | 1.679 | 1.046e-06 | 0.004132 | 423 | 110 | Ccl7,Ifit3,Tlr2,Cfi,LOC497963,Slpi,C1s,Isg15,Masp1,Ccl3 |
| GO_IMMUNE_EFFECTOR_PROCESS | 1.6 | 1.059e-06 | 0.004183 | 368 | 83 | Il6,Ifit3,Cxcl6,Cfi,LOC103692716,C1s,Isg15,Masp1,Ifit1bl,Ccl3 |
| GO_ACTIN_CYTOSKELETON | 1.598 | 1.062e-06 | 0.004192 | 361 | 66 | LOC100909761,Mylpf,Cttn,Myh8,Abra,Mybpc2,Tnni2,Myoz1,Myl1,Myh1 |
| GO_RESPONSE_TO_BACTERIUM | 1.584 | 1.068e-06 | 0.004217 | 341 | 104 | Il6,Tnfsf8,Tlr2,Cxcl6,Il1b,Arg1,LOC497963,Ptgs2,Ptges,Slpi,Isg15,Junb,Cxcl13,Tspo,Ccl3 |
| GO_CYTOKINE_MEDIATED_SIGNALING_PATHWAY | 1.726 | 1.074e-06 | 0.004243 | 321 | 92 | Il6,Ccl7,Ifit3,Cxcl6,Il1b,Il1r2,Isg15,Il1r1,Cxcl13,Ccl3 |
| GO_REGULATION_OF_SYSTEM_PROCESS | 1.634 | 1.075e-06 | 0.004244 | 320 | 102 | Il6,Il1b,Agtr2,Cttn,LOC497963,Errfi1,Ptgs2,LOC103692716,Tnni2,Ccl3 |
| GO_INFLAMMATORY_RESPONSE | 1.67 | 1.075e-06 | 0.004247 | 318 | 105 | Il6,Ccl7,Rarres2,Tlr2,Cxcl6,Il1b,Agtr2,Ptgs2,Ptges,Cxcl13,Tnfaip6,Nfkbiz,Ccl3 |
| GO_REGULATION_OF_RESPONSE_TO_WOUNDING | 1.769 | 1.08e-06 | 0.004263 | 308 | 97 | Il6,Ccl7,Tlr2,Cfi,Il1b,LOC497963,Ptgs2,Masp1,Il1r1,Tnfaip6,Wfdc1,Ccl3 |
| GO_EXTRACELLULAR_MATRIX | 1.783 | 1.086e-06 | 0.004287 | 292 | 123 | Mmp3,Angptl4,Rarres2,Adamts16,LOC108348074,Slpi,LOC103692716,Adamts15,Vwa1,Adamts1,Tgfbi |
| GO_RESPONSE_TO_MOLECULE_OF_BACTERIAL_ORIGIN | 1.682 | 1.105e-06 | 0.004365 | 250 | 79 | Il6,Tlr2,Cxcl6,Il1b,Arg1,LOC497963,Ptgs2,Ptges,Slpi,Junb,Cxcl13,Tspo,Ccl3 |
| GO_PROTEINACEOUS_EXTRACELLULAR_MATRIX | 1.768 | 1.113e-06 | 0.004393 | 237 | 101 | Mmp3,Angptl4,Adamts16,LOC108348074,Adamts15,Vwa1,Adamts1,Tgfbi |
| GO_REGULATION_OF_INFLAMMATORY_RESPONSE | 1.85 | 1.124e-06 | 0.004439 | 218 | 79 | Il6,Ccl7,Tlr2,Cfi,Il1b,LOC497963,Ptgs2,Masp1,Il1r1,Tnfaip6,Wfdc1,Ccl3 |
| GO_MUSCLE_SYSTEM_PROCESS | 1.925 | 1.141e-06 | 0.004507 | 194 | 73 | LOC100909761,Il1b,Agtr2,Mylpf,Myh8,LOC103692716,Mybpc2,Tnni2,Myl1,Myh1 |
| GO_REGULATION_OF_ERK1_AND_ERK2_CASCADE | 1.709 | 1.159e-06 | 0.004578 | 173 | 46 | Il6,Ccl7,Il1b,Errfi1,Scimp,Ccl3 |
| GO_CONTRACTILE_FIBER | 1.925 | 1.169e-06 | 0.004616 | 163 | 63 | LOC100909761,Mylpf,Myh8,Abra,Tnni2,Myl1,Myh1 |
| GO_MUSCLE_CONTRACTION | 1.973 | 1.172e-06 | 0.004629 | 160 | 67 | LOC100909761,Mylpf,Myh8,LOC103692716,Mybpc2,Tnni2,Myl1,Myh1 |
| GO_CELLULAR_RESPONSE_TO_BIOTIC_STIMULUS | 1.717 | 1.195e-06 | 0.00472 | 139 | 42 | Il6,Tlr2,Il1b,Arg1,LOC497963,Tspo,Ccl3 |
| GO_DEFENSE_RESPONSE_TO_VIRUS | 1.734 | 1.214e-06 | 0.004793 | 125 | 26 | Il6,Ifit3,Isg15,Ifit1bl |
| GO_POSITIVE_REGULATION_OF_RESPONSE_TO_WOUNDING | 1.829 | 1.236e-06 | 0.004882 | 110 | 41 | Il6,Ccl7,Tlr2,Il1b,Ptgs2,Ccl3 |
| GO_RESPONSE_TO_INTERFERON_GAMMA | 1.9 | 1.244e-06 | 0.004913 | 105 | 38 | Ccl7,LOC497963,Ccl3 |
| GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA | 1.93 | 1.284e-06 | 0.00507 | 84 | 33 | Ccl7,LOC497963,Ccl3 |
| GO_LEUKOCYTE_CHEMOTAXIS | 1.813 | 1.301e-06 | 0.005137 | 77 | 33 | Il6,Ccl7,Il1b,Cxcl13,Ccl3 |
| GO_POSITIVE_REGULATION_OF_INFLAMMATORY_RESPONSE | 1.874 | 1.306e-06 | 0.005156 | 75 | 35 | Il6,Ccl7,Tlr2,Il1b,Ptgs2,Ccl3 |
| GO_CELLULAR_RESPONSE_TO_INTERLEUKIN_1 | 1.888 | 1.335e-06 | 0.005272 | 64 | 31 | Il6,Ccl7,Has2,Il1r1,Ccl3 |
| GO_PEPTIDASE_ACTIVITY | 1.524 | 2.099e-06 | 0.008291 | 408 | 96 | Mmp3,Adamts16,Ctsl,Cfi,C1s,Adamts15,Masp1,Adamts1,Ctss,Pcsk5 |
| GO_POSITIVE_REGULATION_OF_DEFENSE_RESPONSE | 1.602 | 2.171e-06 | 0.008573 | 292 | 66 | Il6,Ccl7,Tlr2,Il1b,Ptgs2,Ctss,Ccl3 |
| GO_POSITIVE_REGULATION_OF_ERK1_AND_ERK2_CASCADE | 1.709 | 2.442e-06 | 0.009645 | 120 | 38 | Il6,Ccl7,Il1b,Scimp,Ccl3 |
| GO_REGULATION_OF_CYTOKINE_SECRETION | 1.737 | 2.505e-06 | 0.009894 | 100 | 38 | Il6,Tlr2,Il1b,Agtr2,Ccl3 |
Enrichment score for the most highly ranked C2 geneset As this peak was relatively far from the significantly DE genes, this is not a partiularly compelling result
| Pathway | NES | \(p\) | \(p_{adj}\) | size | sizeAtMax | DE |
|---|---|---|---|---|---|---|
| GSE42021_TCONV_PLN_VS_TREG_PRECURSORS_THYMUS_DN | 1.785 | 1.144e-06 | 0.005574 | 192 | 49 | Ccl7,Angptl4,Il1b,Errfi1,Ptgs2,Ptges,LOC103692716,Junb,Nfkbiz |
| GSE22935_WT_VS_MYD88_KO_MACROPHAGE_UP | 1.733 | 1.145e-06 | 0.005577 | 191 | 58 | Ptgs2 |
| GSE42021_TREG_PLN_VS_CD24INT_TREG_THYMUS_UP | 1.837 | 1.146e-06 | 0.005582 | 190 | 59 | Il1b,Errfi1,Ptgs2,Ptges,LOC103692716,Junb,Nfkbiz |
| GSE18281_SUBCAPSULAR_VS_CENTRAL_CORTICAL_REGION_OF_THYMUS_DN | 1.687 | 1.147e-06 | 0.005589 | 188 | 53 | Ifit3,Cxcl6,Ifit1bl,Nfkbiz |
| GSE27434_WT_VS_DNMT1_KO_TREG_DN | 1.809 | 1.149e-06 | 0.005598 | 186 | 44 | Ccl7,Il1b,Errfi1,Ptgs2,LOC103692716,Junb,Nfkbiz |
| GSE14769_UNSTIM_VS_60MIN_LPS_BMDM_DN | 1.705 | 1.15e-06 | 0.005602 | 185 | 53 | Ccl7,Tlr2,Il1b,Errfi1,Ptgs2,Sod2 |
| GSE3039_ALPHAALPHA_VS_ALPHABETA_CD8_TCELL_UP | 1.726 | 1.151e-06 | 0.005606 | 184 | 52 | Il6,Tlr2,Ctsl,Ptges,LOC100911515 |
| GSE14769_UNSTIM_VS_40MIN_LPS_BMDM_DN | 1.757 | 1.153e-06 | 0.005619 | 181 | 53 | Ccl7,Tlr2,Errfi1,Ptgs2,Junb,Nfkbiz |
| GSE45365_NK_CELL_VS_CD11B_DC_DN | 1.785 | 1.155e-06 | 0.005627 | 179 | 54 | Il6,Il1b,Ptges,Junb,Nfkbiz |
| GSE14769_UNSTIM_VS_80MIN_LPS_BMDM_DN | 1.766 | 1.156e-06 | 0.005631 | 178 | 59 | Tlr2,Il1b,Isg15,Sod2,Adamts1 |
| GSE19198_CTRL_VS_IL21_TREATED_TCELL_24H_UP | 1.762 | 1.156e-06 | 0.005631 | 178 | 54 | Mmp3,Il6,Ccl7,Errfi1,Sod2 |
| GSE46606_UNSTIM_VS_CD40L_IL2_IL5_1DAY_STIMULATED_IRF4HIGH_SORTED_BCELL_DN | 1.724 | 1.156e-06 | 0.005631 | 178 | 42 | Il6,Il1b,Errfi1,Ptgs2,Nfkbiz |
| GSE18281_CORTICAL_VS_MEDULLARY_THYMOCYTE_UP | 1.731 | 1.158e-06 | 0.00564 | 176 | 58 | Ifit3,Cxcl6,Arg1,Ptgs2,Slpi,Isg15,Ifit1bl,Ctss |
| GSE42021_TREG_PLN_VS_CD24HI_TREG_THYMUS_UP | 1.827 | 1.159e-06 | 0.005648 | 174 | 55 | Ccl7,Il1b,Errfi1,Ptgs2,LOC103692716,Junb,Nfkbiz |
| GSE32986_CURDLAN_HIGHDOSE_VS_GMCSF_AND_CURDLAN_HIGHDOSE_STIM_DC_DN | 1.719 | 1.16e-06 | 0.005652 | 173 | 58 | Rarres2,Tlr2,Il1b,Ptgs2,Isg15,Sod2,Junb,Nfkbiz |
| GSE9316_IL6_KO_VS_IFNG_KO_INVIVO_EXPANDED_CD4_TCELL_DN | 1.831 | 1.161e-06 | 0.005657 | 172 | 57 | Ccl7,Ptges,Tspo,Nfkbiz |
| GSE42021_CD24HI_TREG_VS_CD24HI_TCONV_THYMUS_DN | 1.805 | 1.162e-06 | 0.005662 | 171 | 59 | Ccl7,Il1b,Errfi1,Ptgs2,LOC103692716,Junb,Nfkbiz |
| GSE9988_LOW_LPS_VS_CTRL_TREATED_MONOCYTE_UP | 1.682 | 1.179e-06 | 0.005743 | 154 | 63 | Il6,Il1b,Errfi1,Ptgs2,Sod2,Tnfaip6,G0s2,Nfkbiz,Ccl3 |
| GSE9988_ANTI_TREM1_VS_ANTI_TREM1_AND_LPS_MONOCYTE_DN | 1.683 | 1.184e-06 | 0.005771 | 149 | 58 | Il6,Il1b,Ptgs2,Sod2,Tnfaip6,G0s2,Nfkbiz |
| GSE2585_CD80_HIGH_VS_LOW_AIRE_KO_MTEC_UP | 1.728 | 1.184e-06 | 0.005771 | 149 | 58 | Il6,LOC497963,C1s,LOC100911515,Tgfbi,Nfkbiz |
| GSE9601_NFKB_INHIBITOR_VS_PI3K_INHIBITOR_TREATED_HCMV_INF_MONOCYTE_DN | 1.914 | 1.184e-06 | 0.005771 | 149 | 50 | Mmp3,Ccl7,Ifit3,Medag,Ptgs2,Sod2 |
| GSE21360_SECONDARY_VS_QUATERNARY_MEMORY_CD8_TCELL_UP | 1.791 | 1.184e-06 | 0.005771 | 149 | 61 | Il6,Ccl7,Il1b,LOC497963,Ptgs2,Ptges,Sod2,Nfkbiz,Ccl3 |
| GSE36888_UNTREATED_VS_IL2_TREATED_TCELL_17H_DN | 1.712 | 1.191e-06 | 0.005803 | 143 | 44 | Il6,Tlr2,Cxcl6,Ptgs2,Ptges,Sod2,Tnfaip6,G0s2,Nfkbiz |
| GSE36891_POLYIC_TLR3_VS_PAM_TLR2_STIM_PERITONEAL_MACROPHAGE_UP | 1.832 | 1.241e-06 | 0.006047 | 107 | 42 | Mmp3,Il6,Ccl7,Ptgs2,Adamts1,Junb,Nfkbiz |
Enrichment score for the most highly ranked C2 geneset As this peak was relatively far from the significantly DE genes, this is not a partiularly compelling result
R version 3.5.2 (2018-12-20)
**Platform:** x86_64-pc-linux-gnu (64-bit)
locale: LC_CTYPE=en_AU.UTF-8, LC_NUMERIC=C, LC_TIME=en_AU.UTF-8, LC_COLLATE=en_AU.UTF-8, LC_MONETARY=en_AU.UTF-8, LC_MESSAGES=en_AU.UTF-8, LC_PAPER=en_AU.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_AU.UTF-8 and LC_IDENTIFICATION=C
attached base packages: stats4, parallel, stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: fgsea(v.1.8.0), Rcpp(v.1.0.1), ggrepel(v.0.8.0), plyranges(v.1.2.0), rtracklayer(v.1.42.2), GenomicRanges(v.1.34.0), GenomeInfoDb(v.1.18.2), IRanges(v.2.16.0), S4Vectors(v.0.20.1), scales(v.1.0.0), ngsReports(v.0.99.7), BiocGenerics(v.0.28.0), pander(v.0.6.3), magrittr(v.1.5), forcats(v.0.4.0), stringr(v.1.4.0), dplyr(v.0.8.0.1), purrr(v.0.3.2), readr(v.1.3.1), tidyr(v.0.8.3), tibble(v.2.1.1), ggplot2(v.3.1.0), tidyverse(v.1.2.1), edgeR(v.3.24.3) and limma(v.3.38.3)
loaded via a namespace (and not attached): nlme(v.3.1-137), bitops(v.1.0-6), matrixStats(v.0.54.0), lubridate(v.1.7.4), RColorBrewer(v.1.1-2), httr(v.1.4.0), tools(v.3.5.2), backports(v.1.1.3), R6(v.2.4.0), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.1.2), gridExtra(v.2.3), tidyselect(v.0.2.5), compiler(v.3.5.2), cli(v.1.1.0), rvest(v.0.3.2), Biobase(v.2.42.0), Cairo(v.1.5-9), xml2(v.1.2.0), DelayedArray(v.0.8.0), plotly(v.4.8.0), ggdendro(v.0.1-20), labeling(v.0.3), digest(v.0.6.18), Rsamtools(v.1.34.1), rmarkdown(v.1.12), XVector(v.0.22.0), pkgconfig(v.2.0.2), htmltools(v.0.3.6), highr(v.0.8), htmlwidgets(v.1.3), rlang(v.0.3.2), readxl(v.1.3.1), rstudioapi(v.0.10), shiny(v.1.2.0), generics(v.0.0.2), zoo(v.1.8-5), hwriter(v.1.3.2), jsonlite(v.1.6), crosstalk(v.1.0.0), BiocParallel(v.1.16.6), RCurl(v.1.95-4.12), GenomeInfoDbData(v.1.2.0), Matrix(v.1.2-17), Rhdf5lib(v.1.4.3), munsell(v.0.5.0), stringi(v.1.4.3), yaml(v.2.2.0), MASS(v.7.3-51.1), SummarizedExperiment(v.1.12.0), zlibbioc(v.1.28.0), rhdf5(v.2.26.2), plyr(v.1.8.4), grid(v.3.5.2), promises(v.1.0.1), crayon(v.1.3.4), lattice(v.0.20-38), Biostrings(v.2.50.2), haven(v.2.1.0), hms(v.0.4.2), locfit(v.1.5-9.1), knitr(v.1.22), pillar(v.1.3.1), fastmatch(v.1.1-0), XML(v.3.98-1.19), glue(v.1.3.1), evaluate(v.0.13), ShortRead(v.1.40.0), latticeExtra(v.0.6-28), data.table(v.1.12.0), modelr(v.0.1.4), httpuv(v.1.5.0), cellranger(v.1.1.0), gtable(v.0.3.0), assertthat(v.0.2.1), xfun(v.0.5), mime(v.0.6), xtable(v.1.8-3), broom(v.0.5.1), later(v.0.8.0), viridisLite(v.0.3.0), truncnorm(v.1.0-8) and GenomicAlignments(v.1.18.1)